# HG changeset patch
# User iuc
# Date 1569966812 14400
# Node ID 29bdbc353f20a8433031abeaa02f64d362915a12
# Parent  95219305823aac326239d6a8693f698eed1f9356
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth commit 823259bba9405d22dc2add24746057122c819ad3"

diff -r 95219305823a -r 29bdbc353f20 bwameth.xml
--- a/bwameth.xml	Thu Nov 09 13:07:16 2017 -0500
+++ b/bwameth.xml	Tue Oct 01 17:53:32 2019 -0400
@@ -1,86 +1,85 @@
-<tool id="bwameth" name="bwameth" version="0.2.0.4" profile="17.01">
+<tool id="bwameth" name="bwameth" version="@TOOL_VERSION@" profile="17.01">
     <description>Fast and accurate aligner of BS-Seq reads.</description>
+    <macros>
+        <token name="@TOOL_VERSION@">0.2.2</token>
+    </macros>
     <requirements>
-        <requirement type="package" version="0.2.0">bwameth</requirement>
-        <requirement type="package" version="0.7.16">bwa</requirement>
+        <requirement type="package" version="@TOOL_VERSION@">bwameth</requirement>
     </requirements>
     <version_command>bwameth.py --version</version_command>
-    <command detect_errors="aggressive">
-<![CDATA[
-    #if $referenceSource.source != "indexed":
-        mkdir index_dir &&
-        ln -s '$referenceSource.reference' index_dir/genome.fa &&
-        bwameth.py index index_dir/genome.fa &&
-        #set index="index_dir/genome.fa"
-    #else
-        #set index=$referenceSource.index.fields.path
-    #end if
+    <command detect_errors="aggressive"><![CDATA[
+#if $referenceSource.source != "indexed":
+    mkdir index_dir &&
+    ln -s '$referenceSource.reference' index_dir/genome.fa &&
+    bwameth.py index index_dir/genome.fa &&
+    #set index="index_dir/genome.fa"
+#else
+    #set index=$referenceSource.index.fields.path
+#end if
 
-    ## Link in the files with a name that's appropriate
-    #if str($single_or_paired.single_or_paired_opts) == 'paired':
-        #if $single_or_paired.input_mate1.is_of_type("fastq.gz", "fastqsanger.gz"):
-            #set read1 = "input_f.fastq.gz"
-        #else if $single_or_paired.input_mate1.is_of_type("fastq.bz2", "fastqsanger.bz2"):
-            #set read1 = "input_f.fastq.bz2"
-        #else:
-            #set read1 = "input_f.fastq"
-        #end if
-        ln -f -s '${single_or_paired.input_mate1}' ${read1} &&
+## Link in the files with a name that's appropriate
+#if str($single_or_paired.single_or_paired_opts) == 'paired':
+    #if $single_or_paired.input_mate1.is_of_type("fastq.gz", "fastqsanger.gz"):
+        #set read1 = "input_f.fastq.gz"
+    #else if $single_or_paired.input_mate1.is_of_type("fastq.bz2", "fastqsanger.bz2"):
+        #set read1 = "input_f.fastq.bz2"
+    #else:
+        #set read1 = "input_f.fastq"
+    #end if
+    ln -f -s '${single_or_paired.input_mate1}' ${read1} &&
 
-        #if $single_or_paired.input_mate2.is_of_type("fastq.gz", "fastqsanger.gz"):
-            #set read2 = "input_r.fastq.gz"
-        #else if $single_or_paired.input_mate2.is_of_type("fastq.bz2", "fastqsanger.bz2"):
-            #set read2 = "input_r.fastq.bz2"
-        #else:
-            #set read2 = "input_r.fastq"
-        #end if
-        ln -f -s '${single_or_paired.input_mate2}' ${read2} &&
-    #else if str($single_or_paired.single_or_paired_opts) == 'paired_collection':
-        #if $single_or_paired.input_mate1.forward.is_of_type("fastq.gz", "fastqsanger.gz"):
-            #set read1 = "input_f.fastq.gz"
-        #else if $single_or_paired.input_mate1.forward.is_of_type("fastq.bz2", "fastqsanger.bz2"):
-            #set read1 = "input_f.fastq.bz2"
-        #else:
-            #set read1 = "input_f.fastq"
-        #end if
-        ln -s '${single_or_paired.input_mate1.forward}' ${read1} &&
+    #if $single_or_paired.input_mate2.is_of_type("fastq.gz", "fastqsanger.gz"):
+        #set read2 = "input_r.fastq.gz"
+    #else if $single_or_paired.input_mate2.is_of_type("fastq.bz2", "fastqsanger.bz2"):
+        #set read2 = "input_r.fastq.bz2"
+    #else:
+        #set read2 = "input_r.fastq"
+    #end if
+    ln -f -s '${single_or_paired.input_mate2}' ${read2} &&
+#else if str($single_or_paired.single_or_paired_opts) == 'paired_collection':
+    #if $single_or_paired.input_mate1.forward.is_of_type("fastq.gz", "fastqsanger.gz"):
+        #set read1 = "input_f.fastq.gz"
+    #else if $single_or_paired.input_mate1.forward.is_of_type("fastq.bz2", "fastqsanger.bz2"):
+        #set read1 = "input_f.fastq.bz2"
+    #else:
+        #set read1 = "input_f.fastq"
+    #end if
+    ln -s '${single_or_paired.input_mate1.forward}' ${read1} &&
 
-        #if $single_or_paired.input_mate1.reverse.is_of_type("fastq.gz", "fastqsanger.gz"):
-            #set read2 = "input_r.fastq.gz"
-        #else if $single_or_paired.input_mate1.reverse.is_of_type("fastq.bz2", "fastqsanger.bz2"):
-            #set read2 = "input_r.fastq.bz2"
-        #else:
-            #set read2 = "input_r.fastq"
-        #end if
-        ln -s '${single_or_paired.input_mate1.reverse}' ${read2} &&
+    #if $single_or_paired.input_mate1.reverse.is_of_type("fastq.gz", "fastqsanger.gz"):
+        #set read2 = "input_r.fastq.gz"
+    #else if $single_or_paired.input_mate1.reverse.is_of_type("fastq.bz2", "fastqsanger.bz2"):
+        #set read2 = "input_r.fastq.bz2"
     #else:
-        #if $single_or_paired.input_singles.is_of_type("fastq.gz", "fastqsanger.gz"):
-            #set read1 = "input_f.fastq.gz"
-        #else if $single_or_paired.input_singles.is_of_type("fastq.bz2", "fastqsanger.bz2"):
-            #set read1 = "input_f.fastq.bz2"
-        #else:
-            #set read1 = "input_f.fastq"
-        #end if
-        ln -f -s '${single_or_paired.input_singles}' ${read1} &&
+        #set read2 = "input_r.fastq"
     #end if
-
+    ln -s '${single_or_paired.input_mate1.reverse}' ${read2} &&
+#else:
+    #if $single_or_paired.input_singles.is_of_type("fastq.gz", "fastqsanger.gz"):
+        #set read1 = "input_f.fastq.gz"
+    #else if $single_or_paired.input_singles.is_of_type("fastq.bz2", "fastqsanger.bz2"):
+        #set read1 = "input_f.fastq.bz2"
+    #else:
+        #set read1 = "input_f.fastq"
+    #end if
+    ln -f -s '${single_or_paired.input_singles}' ${read1} &&
+#end if
 
-    bwameth.py
-        -t "\${GALAXY_SLOTS:-4}"
-        --reference "${index}"
+bwameth.py
+-t "\${GALAXY_SLOTS:-4}"
+--reference '${index}'
 
-    #if str($readGroup).strip() != "":
-        --read-group "${readGroup}"
-    #end if
+#if str($readGroup).strip():
+    --read-group '${readGroup}'
+#end if
 
-    #if $single_or_paired.single_or_paired_opts == 'single':
-        $read1
-    #else:
-        $read1 $read2
-    #end if
-    | samtools view -u - | samtools sort -@ "\${GALAXY_SLOTS:-4}" -T tmp -O bam -o output.bam -
-]]>
-    </command>
+#if $single_or_paired.single_or_paired_opts == 'single':
+    $read1
+#else:
+    $read1 $read2
+#end if
+| samtools view -u - | samtools sort -@ "\${GALAXY_SLOTS:-4}" -T "\${TMPDIR:-.}" -O bam -o output.bam -
+    ]]></command>
     <inputs>
         <conditional name="referenceSource">
             <param name="source" type="select" label="Select a genome reference from your history or a built-in index?">
@@ -146,14 +145,12 @@
             <output file="output.bam" ftype="bam" name="output" lines_diff="2"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 **What it does**
 
 BWA-meth performs alignment of reads in a bisulfite-sequencing experiment (e.g., RRBS or WGBS) to a genome. The methodology employed for this is similar to bismark, where both the reads and the reference genome are *in silico* converted prior to alignment. Methylation extraction on the resulting BAM file can be done with the PileOMeth tool.
-]]>
-    </help>
+    ]]></help>
     <citations>
         <citation type="bibtex">@misc{1401.1129,
         Author = {Brent S. Pedersen and Kenneth Eyring and Subhajyoti De and Ivana V. Yang and David A. Schwartz},